isoCounts: Create count matrix with different summarizing options

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Create count matrix with different summarizing options

Description

This function collapses isomiRs into different groups. It is a similar concept than how to work with gene isoforms. With this function, different changes can be put together into a single miRNA variant. For instance all sequences with variants at 3' end can be considered as different elements in the table or analysis having the following naming ⁠hsa-miR-124a-5p.iso.t3:AAA⁠.

Usage

isoCounts(
  ids,
  ref = FALSE,
  iso5 = FALSE,
  iso3 = FALSE,
  add = FALSE,
  snv = FALSE,
  seed = FALSE,
  all = FALSE,
  minc = 1,
  mins = 1,
  merge_by = NULL
)

Arguments

ids	Object of class IsomirDataSeq.
ref	Differentiate reference miRNA from rest.
iso5	Differentiate trimming at 5 miRNA from rest.
iso3	Differentiate trimming at 3 miRNA from rest.
add	Differentiate additions miRNA from rest.
snv	Differentiate nt substitution miRNA from rest.
seed	Differentiate changes in 2-7 nts from rest.
all	Differentiate all isomiRs.
minc	Int minimum number of isomiR sequences to be included.
mins	Int minimum number of samples with number of sequences bigger than minc counts.
merge_by	Column in coldata to merge samples into a single column in counts. Useful to combine technical replicates.

Details

You can merge all isomiRs into miRNAs by calling the function only with the first parameter isoCounts(ids). You can get a table with isomiRs altogether and the reference miRBase sequences by calling the function with ref=TRUE. You can get a table with 5' trimming isomiRS, miRBase reference and the rest by calling with isoCounts(ids, ref=TRUE, iso5=TRUE). If you set up all parameters to TRUE, you will get a table for each different sequence mapping to a miRNA (i.e. all isomiRs).

Examples for the naming used for the isomiRs are at http://seqcluster.readthedocs.org/mirna_annotation.html#mirna-annotation.

Value

IsomirDataSeq object with new count table. The count matrix can be access with counts(ids).

Examples

data(mirData)
ids <- isoCounts(mirData, ref=TRUE)
head(counts(ids))
# taking into account isomiRs and reference sequence.
ids <- isoCounts(mirData, ref=TRUE, minc=10, mins=6)
head(counts(ids))

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.